first commit

defaults

+{
+    "PP2GeneList":"oss://pgx-reference-data/reference/charger/hg38_PP2_152_gene_list.txt",
+    "clinvar":"oss://pgx-reference-data/reference/charger/clinvar_alleles.single.b38.tsv.gz",
+    "HotSpot3D":"oss://pgx-reference-data/reference/charger/MC3.noHypers.mericUnspecified.d10.r20.v114.grch38liftOver.clusters",
+    "pathogenic":"oss://pgx-reference-data/reference/charger/emptyRemoved_20160428_pathogenic_variants_HGVSg_VEP_grch38lifOver.vcf",
+    "inheritanceGeneList":"oss://pgx-reference-data/reference/charger/hg38_inheritanceGeneList.txt",
+    "charger_docker":"registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/charger:0.5.4",
+    "disk_size":"200",
+    "charger_cluster":"OnDemand bcs.ps.r.xlarge img-ubuntu-vpc"
+}
+

inputs

+{
+  "{{ project_name }}.sample_id": "{{ sample_id }}",
+  "{{ project_name }}.vep_vcf": "{{ vep_vcf }}",
+  "{{ project_name }}.PP2GeneList": "{{ PP2GeneList }}",
+  "{{ project_name }}.clinvar": "{{ clinvar }}",
+  "{{ project_name }}.HotSpot3D": "{{ HotSpot3D }}",
+  "{{ project_name }}.pathogenic": "{{ pathogenic }}",
+  "{{ project_name }}.inheritanceGeneList": "{{ inheritanceGeneList }}",
+  "{{ project_name }}.charger_cluster": "{{ charger_cluster }}",
+  "{{ project_name }}.charger_docker": "{{ charger_docker }}",
+  "{{ project_name }}.disk_size": "{{ disk_size }}"
+}
+

tasks/charger.wdl

+task charger{
+    String sample_id 
+    File vep_vcf
+    File inheritanceGeneList
+    File clinvar
+    File pathogenic
+    File HotSpot3D
+    File PP2GeneList
+
+    String disk_size
+    String docker
+    String cluster
+
+    command <<<
+	
+        set -o pipefail
+        set -e
+
+        vep_index=`echo ${vep_vcf}|awk -F "/" '{print $NF}'|sed 's/.vcf//'`
+
+        echo ${sample_id}
+
+        mkdir ./output/
+        charger -f ${vep_vcf} \
+            -o ./output/$vep_index.charger.tsv \
+            -D ${inheritanceGeneList} \
+            -l --mac-clinvar-tsv ${clinvar} \
+            -z ${pathogenic} \
+            -H ${HotSpot3D} \
+            --PP2GeneList ${PP2GeneList}
+ 
+ 
+    >>>
+	
+    runtime {
+        docker: docker
+        cluster: cluster
+        systemDisk: "cloud_ssd 40"
+        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+
+    output {
+        Array[File] filter_result=glob("./output/${sample_id}*")
+    }
+
+}
+
+

workflow.wdl

+import "./tasks/charger.wdl" as charger
+
+workflow run_charger {
+    String sample_id
+    File vep_vcf
+    File inheritanceGeneList
+    File clinvar
+    File pathogenic
+    File HotSpot3D
+    File PP2GeneList
+
+    String disk_size
+    String charger_docker
+    String charger_cluster
+
+        call charger.charger as charger {
+                input:	
+                sample_id=sample_id,
+                vep_vcf=vep_vcf,
+                inheritanceGeneList=inheritanceGeneList,
+                clinvar=clinvar,
+                pathogenic=pathogenic,
+                HotSpot3D=HotSpot3D,
+                PP2GeneList=PP2GeneList,
+                docker=charger_docker,
+                cluster=charger_cluster,
+                disk_size=disk_size
+        }
+
+
+}	
+